The Shadow War, or the Shadowling Civil War, is a conflict in which the Spriggat Dissidents rebelled from the Shadowling Empire in an attempt to regain their once-lost indpendence from the shadowlings.
Long ago, the spriggats used to have their own state-nation called Spriggatia. The spriggat independence was ended when the militaristic Shadowling Empire conquered and annexed Spriggatia. Under the rule of the Shadowling Queen, the spriggats were treated as an underclass. Female spriggats were even killed to ensure that the Queen had absolute control over the race.
Starting early in the war, the shadowlings started abducting students from the Psy Academy in order to use them against the Dissidents. The Hero of Chapter 1 & 2 becomes an active participant in the war after the Hero's little brother, David, is kidnapped by the shadowlings. The Hero rescues David from his captures only to find that David has already been wiped into a mindless shell. In exchange for returning David back to normal, the Hero agrees to become the personal slave of the shadowling general Tastidian for three years.
To try to gain an edge over the Shadowling Empire, the Dissidents hire the human mercenary group, The Mechanics. Tastidian awakens the Hero, now his slave, to eliminate the new threat. Under Tastidian's orders, the Hero's team uncovers that the Mechanics are building a new weapon called "Energy Golems". Because the new golems can accurately strike multiple targets over long distances, the Dissidents and their allies gained a tactical advantage by building them. The Hero's team reversed this advantage by destroying the Mechanics' Energy Golem Workshop and by looting an inoperative Energy Golem to be reverse engineered by the Shadowling Empire.
Battles at Lake Alto
After a series of battles at Lake Alto, the Dissident leader Cerzak defeats his shadowling rival General Darkeye. To ensure that reinforcements don't get to the wounded shadowling general, the Dissidents lay a minefield throughout the lake. Fresh from destroying the Golem Workshop, the Hero is sent by his master to use a psy boat to navigate through the minefield and rescue Darkeye. After reaching the wounded Darkeye, the Hero's team is forced to fight and defeat Cerzak and his fellow spriggats. After Cerzak has fallen, the Hero pilots the psy boat back through the minefield and returns Darkeye to safety.
The Queen's fall
With Cerzak defeated and the shadowlings producing energy golems, there was little hope for a Dissident victory. Desperate for help, the spriggats send emissaries to the Psy Academy. Tastidian learns of this and sends the Hero to convince the Psy Academy of the foolishness of joining the Dissidents. After arriving at the Psy Academy, the Hero becomes free of the slave bracelet. Finally free, the Hero talks to Dean Lukas who informs the Hero that the Psy Academy has sided with the spriggats to stop the shadowling abductions of academy students. The Hero and the rest of the team decide to join the Psy Academy in opposition to the Shadowling Empire. Following Lukas's plan, the Psy Academy and the remaining spriggats stage a final stand to divert most of the shadowling forces away from Somnus, while the Hero's team assaults the Queen's Palace and kills Tastidian and the Shadowling Queen.
With Tastidian and the Shadowling Queen gone, the spriggats were at last able to return to Somnus. In accordance with Cerzak's wishes they established a constitutional democracy over the Shadowlands. The new Shadowling Republic was based on Spriggat-Shadowling equality. Many Shadowling Loyalists loathe the new republic and long for the return of the long-dead Queen's rule. These Loyalists constantly try to undermine the Shadowling Republic.